IR Z Probe not very repeatable, nozzle crashed again

I am using one of these Z probes mounted on my custom mounting bracket on the E3Dv6 hot-end (with a DiiiCooler between the probe and the nozzle).

Previously it was quite repeatable, but lately it is struggling to trigger at the same height. Right now, I successfully homed the printer quite a few times (specifically to accurately calculate the probing distance, and set it, then test it a few times to ensure it is correct etc). I started a print, which failed due to an extruder issue, and when restarting, the probe did not trigger at the right height while doing the Home, causing the nozzle to crash and ruin my new build surface.

I am using a glass plate with a lamination pouch as my build surface (it works really good and is, luckily, quite cheap). I have used a permanent marker at the positions where the probe will probe to ensure it should trigger (as previously I noticed that sometimes the glass is invisible to it).

The optical components are not contaminated, the probe is about 35mm from the nozzle, so also safe from heat.

The connections seems secure. I am using a 3way DuPont/SIL female connector to connect to it, and it feels secure. On the other side I have the 3 pin KK connector, which also feels secure.

Something I noticed, was that the returned value sometimes also changed. For example it would trigger on 536 (entered into the config), and a next time I run a probe, the value will only go to 535 which also resulted in a nozzle crash as it could not get that 536 value.

Something I noticed, was that the returned value sometimes also changed. For example it would trigger on 536 (entered into the config), and a next time I run a probe, the value will only go to 535 which also resulted in a nozzle crash as it could not get that 536 value.

It's not unusual for the value to change by 1. You should have the threshold set to 500 (that's P500 in the G31 command), so it doesn't matter whether you get 535 or 536 from the sensor.

After also discussing the situation with my brother, I replaced the lamination pouch (and with it my permanent marker marks), and added white stickers at the probe positions (directly on the glass), with the pouch applied over them, and have now been doing a print (after once again homing and calibrating the trigger height) and it started good (still going at time of writing).

An unrelated thing that was bugging me (not very important) is due to my starting G-code, the first 10 layers are seen as the first layer in the interfaces (and then layers 2-10 is completed in 0 seconds). Any way to tell the firmware where the first layer is starting, so that it does not estimate so high Time Left?
The part in my starting G-code that cause this is a line where I extrude a bunch of filament while moving slowly in the Y direction, and being 1.5mm above the bed. This is to prime my nozzle, and in stead of putting it all down at the origin (like some printers/slicers do with factory settings), this leaves a simple fat line, which also clears the outside of the nozzle.
Since I use Simplify3D, the first layer is marked with "; layer 1, Z = 0.150" -> I think if it finds anything like this, it should be the a good hook to start layer counting?

An unrelated thing that was bugging me (not very important) is due to my starting G-code, the first 10 layers are seen as the first layer in the interfaces (and then layers 2-10 is completed in 0 seconds). Any way to tell the firmware where the first layer is starting, so that it does not estimate so high Time Left?
The part in my starting G-code that cause this is a line where I extrude a bunch of filament while moving slowly in the Y direction, and being 1.5mm above the bed. This is to prime my nozzle, and in stead of putting it all down at the origin (like some printers/slicers do with factory settings), this leaves a simple fat line, which also clears the outside of the nozzle.
Since I use Simplify3D, the first layer is marked with "; layer 1, Z = 0.150" -> I think if it finds anything like this, it should be the a good hook to start layer counting?